[2024-01-24 11:26:54,318] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,322] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,322] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f114fcc-1731-49d6-a7d6-dffa71dda955/dqc_reference
[2024-01-24 11:26:58,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,224] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,224] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6e0ba67-7a2a-496f-8511-bf31f7914fb0/GCF_023078335.1_ASM2307833v1_genomic.fna.gz | prodigal -d GCF_023078335.1_ASM2307833v1_genomic.fna/cds.fna -a GCF_023078335.1_ASM2307833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:08,626] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:08,627] [INFO] Task started: HMMsearch
[2024-01-24 11:27:08,627] [INFO] Running command: hmmsearch --tblout GCF_023078335.1_ASM2307833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f114fcc-1731-49d6-a7d6-dffa71dda955/dqc_reference/reference_markers.hmm GCF_023078335.1_ASM2307833v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:08,973] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:08,974] [INFO] Found 6/6 markers.
[2024-01-24 11:27:09,022] [INFO] Query marker FASTA was written to GCF_023078335.1_ASM2307833v1_genomic.fna/markers.fasta
[2024-01-24 11:27:09,023] [INFO] Task started: Blastn
[2024-01-24 11:27:09,023] [INFO] Running command: blastn -query GCF_023078335.1_ASM2307833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f114fcc-1731-49d6-a7d6-dffa71dda955/dqc_reference/reference_markers.fasta -out GCF_023078335.1_ASM2307833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:09,634] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:09,638] [INFO] Selected 17 target genomes.
[2024-01-24 11:27:09,638] [INFO] Target genome list was writen to GCF_023078335.1_ASM2307833v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:09,647] [INFO] Task started: fastANI
[2024-01-24 11:27:09,647] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6e0ba67-7a2a-496f-8511-bf31f7914fb0/GCF_023078335.1_ASM2307833v1_genomic.fna.gz --refList GCF_023078335.1_ASM2307833v1_genomic.fna/target_genomes.txt --output GCF_023078335.1_ASM2307833v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:25,770] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:25,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f114fcc-1731-49d6-a7d6-dffa71dda955/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:25,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f114fcc-1731-49d6-a7d6-dffa71dda955/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:25,790] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:25,791] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:25,791] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	100.0	1764	1765	95	conclusive
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	80.7393	683	1765	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	80.4868	696	1765	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	79.7843	477	1765	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	79.7152	628	1765	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	79.6314	616	1765	95	below_threshold
Bacillus weihaiensis	strain=Alg07	GCA_001889165.1	1547283	1547283	type	True	79.5842	460	1765	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	79.4528	590	1765	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_004801455.1	2567941	2567941	type	True	79.0767	459	1765	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	77.3075	127	1765	95	below_threshold
Metabacillus idriensis	strain=DSM-19097	GCA_904423875.1	324768	324768	type	True	77.2541	159	1765	95	below_threshold
Metabacillus idriensis	strain=DSM 19097	GCA_009674765.1	324768	324768	type	True	77.212	157	1765	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	77.1504	124	1765	95	below_threshold
Bacillus oleivorans	strain=JC228	GCA_900207585.1	1448271	1448271	type	True	76.7651	97	1765	95	below_threshold
Bacillus solimangrovi	strain=GH2-4	GCA_001742425.1	1305675	1305675	type	True	76.6503	74	1765	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	76.4657	63	1765	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:25,793] [INFO] DFAST Taxonomy check result was written to GCF_023078335.1_ASM2307833v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:25,793] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:25,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:25,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f114fcc-1731-49d6-a7d6-dffa71dda955/dqc_reference/checkm_data
[2024-01-24 11:27:25,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:25,853] [INFO] Task started: CheckM
[2024-01-24 11:27:25,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023078335.1_ASM2307833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023078335.1_ASM2307833v1_genomic.fna/checkm_input GCF_023078335.1_ASM2307833v1_genomic.fna/checkm_result
[2024-01-24 11:28:01,621] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:01,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:01,644] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:01,644] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:01,645] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023078335.1_ASM2307833v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:01,645] [INFO] Task started: Blastn
[2024-01-24 11:28:01,645] [INFO] Running command: blastn -query GCF_023078335.1_ASM2307833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f114fcc-1731-49d6-a7d6-dffa71dda955/dqc_reference/reference_markers_gtdb.fasta -out GCF_023078335.1_ASM2307833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:02,483] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:02,487] [INFO] Selected 12 target genomes.
[2024-01-24 11:28:02,487] [INFO] Target genome list was writen to GCF_023078335.1_ASM2307833v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:02,500] [INFO] Task started: fastANI
[2024-01-24 11:28:02,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6e0ba67-7a2a-496f-8511-bf31f7914fb0/GCF_023078335.1_ASM2307833v1_genomic.fna.gz --refList GCF_023078335.1_ASM2307833v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023078335.1_ASM2307833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:15,586] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:15,602] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:15,602] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002577655.1	s__Metabacillus sp002577655	95.2516	1265	1765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003667825.1	s__Metabacillus litoralis_B	93.637	1437	1765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_002019635.1	s__Metabacillus halosaccharovorans	80.7303	685	1765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	95.47	95.47	0.86	0.86	2	-
GCF_000518865.1	s__Metabacillus sp000518865	80.2184	657	1765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871465.1	s__Metabacillus sp002871465	80.2003	680	1765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.74	98.74	0.91	0.91	2	-
GCF_014217835.1	s__Metabacillus litoralis_A	79.6869	584	1765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	99.81	99.81	0.98	0.98	2	-
GCF_001889165.1	s__Metabacillus weihaiensis	79.5156	460	1765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	97.24	97.24	0.88	0.88	2	-
GCF_017497975.1	s__Metabacillus sp017497975	79.4504	592	1765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981385.1	s__Metabacillus sp000981385	78.8938	453	1765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259415.1	s__Metabacillus sp003259415	78.8918	390	1765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674765.1	s__Bacillus_P idriensis	77.212	157	1765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	98.40	95.01	0.92	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:15,604] [INFO] GTDB search result was written to GCF_023078335.1_ASM2307833v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:15,604] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:15,609] [INFO] DFAST_QC result json was written to GCF_023078335.1_ASM2307833v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:15,609] [INFO] DFAST_QC completed!
[2024-01-24 11:28:15,609] [INFO] Total running time: 0h1m21s